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"# Using Molecular Geometries\n",
"> ### In this tutorial we will cover:\n",
"> - how we can use BuildAMol's molecular geometries to build fragment molecules from scratch"
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"import plotly\n",
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"Let us first check if we have the molecule available in the built-in resources:"
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"import buildamol as bam\n",
"bam.load_small_molecules()\n",
"\n",
"bam.has_compound(\"PF5\", search_by=\"formula\")"
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"source": [
"Well, if the compound is not available, let us query PubChem for it..."
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"execution_count": 3,
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"source": [
"No matches... Let's try again but with the name"
]
},
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"execution_count": 4,
"metadata": {},
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"bam.query_pubchem(\"phosphorus pentafluoride\")"
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"source": [
"Nope... Well, the SMILES should definitely work, though:"
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"execution_count": 5,
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"text": [
"/Users/noahhk/anaconda3/envs/glyco2/lib/python3.11/site-packages/plotly/express/_core.py:1985: FutureWarning:\n",
"\n",
"When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.\n",
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"Mhmm... Somehow that does not look like the PF5 we were expecting. For starters, there appear to be only four F atoms, and secondly PF5 is supposed to have a trigonal bipyramidal geometry and not whatever this is...\n",
"\n",
"So it seems like we hit a particularly tricky case with this tiny molecule. Can we simply not build it at all? Well, we wouldn't be having this tutorial if that were the case! In fact, to account for exactly such rare use cases where a particular molecule is not available through conventional means, BuildAMol comes with _molecular geometries_ that can be used to define valid coordinates for manual atom placement. \n",
"\n",
"Let's see how this works as we construct PF5!"
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"\n",
"The geometries can be found in the `structural.geometry` submodule. They come with methods that accept one or more atoms to use for referencing the available coordinates and constructing the remaining ones. For our use case we need to use a `trigonal_bipyramidal` geometry. But first, let's just make some atoms to build a PF5 molecule."
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"\n",
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"# we just pass the central P atom as only reference point\n",
"# and let the other coordinates be generated automatically\n",
"# they will be automatically applied onto the atoms that we pass\n",
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"And there we have it, a correctly arranged PF5 molecule! So, we were able to compute valid atom coordinates using the trigonal bipyramidal geometry object and a list of some atoms. The same can be done for any other available geometry. Available are the five main VESPR geometries:\n",
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"When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.\n",
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"source": [
"# reset all coordinates to 0,0,0\n",
"for F in Fs:\n",
" F.coord = bam.structural.origin\n",
"\n",
"# now use the trigonal bipyramidal geometry to arrange the atoms\n",
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" geometry=bam.structural.geometry.trigonal_bipyramidal, \n",
" atoms=[P, *Fs],\n",
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"And with this we again have a PF5 molecule. In fact, this method will automatically fill any vacant atom slots that the geometry provides with hydrogen atoms. \n",
"\n",
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"# now we make a molecule with only two F atoms\n",
"# (actually, these will be in the plane, since we already inferred\n",
"# their coordinates before). The remaining 3 atom slots\n",
"# will be filled with hydrogen atoms.\n",
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" geometry=bam.structural.geometry.trigonal_bipyramidal, \n",
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"And there we have it. With this we have reached the end of this tutorial. We saw how we can use geometries to manually create small molecules with relatively little effort. \n",
"\n",
"Thank's for checking out this tutorial and good luck with your research using BuildAMol!"
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